RNA-seq based characterization of host responses to Brachyspira hyodysenteriae infection

Using RNA-seq, we investigated for the first time the in vivo transcriptome of colonic mucosa in 16 control pigs and 16 pigs experimentally infected with Brachyspira hyodysenteriae, which were euthanized at different stages of the disease: 8 during a preclinical stage characterized by bacterial shedding without clinical signs (early infection group), and 8 during an acute stage presenting with dysentery (acute infection group). No significant differences in gene expression were observed between the control and early infection groups, except for an overexpression of matrix metalloproteinases (MMPs), which may be associated with early ulceration of the colonic epithelium. The acute infection group showed a significant upregulation of the S100A8, S100A9 and S100A12 proteins, but most of the host biological processes were downregulated, particularly those related to the immune response, such as chemokines and cytokines signalling or immune cells chemotaxis and migration. Accordingly, the prediction of cell types associated with the detected transcripts revealed a depletion of immune cells, except neutrophils, and an enrichment of stromal cells in the acute infection group. Marked alterations in mucin gene expression were observed in this group, including overexpression of MUC5AC, MUC20, and GCNT3, a trend toward increased MUC2, and downregulation of MUC1 and MUC3. Although no significant changes were detected in the early infection group, a similar trend was observed. These findings suggest that B. hyodysenteriae may suppress host immune responses, particularly through inhibition of the IFNγ signalling pathway, accompanied by a depletion of cellular responses, except for neutrophils, and promotion of tissue damage via overexpression of multiple MMPs, even at early stages of the disease. Significant alterations in mucin composition were observed during the acute stage, likely driven by the overexpression of S100 proteins and activation of the SPDEF pathway. This study proposes several mechanisms associated with the pathophysiology of swine dysentery, revealing key aspects of host–pathogen interactions, particularly the host response to B. hyodysenteriae infection. Briefly, 32 females crossbred 7 weeks-old piglets (commercial hybrids of Landrace × Large White × Pietrain) from a SD-free farm were randomly assigned to either the control or infected group (n = 16 per group). The infected group was orally challenged for three consecutive days with 30 mL of broth containing B. hyodysenteriae B-204 (ATCC 31212) strain at a concentration of 5 × 10^8 bacteria/mL. Half of the infected pigs (n = 8) were euthanised 24 hours after the first B. hyodysenteriae q-PCR positive in faeces (early infection group), while the other half (n = 8) were euthanised after two consecutive days of mucohaemorrhagic diarrhoea (acute infection group). Non-infected controls (control group) were euthanised and necropsied in parallel, one to one, with the challenged pigs.